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9uem

Metallo-Beta-Lactamase VIM-2 in Complex with MBL/SBL Inhibitor FB1-12

Method: X-RAY DIFFRACTION D_max: 54.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uem
deposition_date	2025-04-08
last_revision	2026-04-15
title	Metallo-Beta-Lactamase VIM-2 in Complex with MBL/SBL Inhibitor FB1-12
keywords	Beta-lactamase, Metallo-Beta-Lactamase VIM-2, VIM-2, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	17.03 Å
rg_electron	16.03 Å
i0	21787700.00
molecular_weight	23579.0 kDa
excluded_volume	22647 Å³
envelope_volume	34318 Å³
shell_volume	17384 Å³
envelope_diameter	55.6 Å
shell_rg	22.73 Å
envelope_rg	16.36 Å
shape_rg	16.01 Å
total_rg	16.84 Å
total_atoms	1783
n_residues	232
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	54.3 Å
rg_real	16.90 Å
rg_real_error	0.29 Å
i0_real	2.1790e+07
i0_real_error	2.4480e+05
rg_reciprocal	16.92 Å
i0_reciprocal	21790000.0000
total_estimate	0.8032
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	22.1 Å
skewness	0.126
kurtosis	-0.393
angular_range	— – 0.4650 Å⁻¹
current_alpha	0.0000
highest_alpha	6927000.0000
n_real_points	77
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.819; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Metallo-beta-lactamase VIM-2
formula_weight	24766.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2010

EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRS

Source

organism	Pseudomonas aeruginosa
ncbi_taxonomy_id	287
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	;9-[1-[~{N}-(2-fluoranylethyl)carbamimidoyl]azetidin-3-yl]oxy-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid ;
formula_weight	368.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	FORMIC ACID
formula_weight	46.0 kDa
src_method	syn
entity_count	4

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	227

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6. Citations (1)

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length_a	91.440 Å
length_b	46.260 Å
length_c	64.190 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	1.800 Å
resolution_low	37.530 Å
r_factor	0.1708
r_work	0.1683
r_free	0.1997

fit	/app/data/saxs_computation/ue/9uem/9uem.fit
pddf	/app/data/pr_computation/ue/9uem/9uem.pr.out
profile	/app/data/saxs_computation/ue/9uem/9uem.dat